Computational host range prediction-The good, the bad, and the ugly.
| Autor: | Howell AA, Versoza CJ; Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA., Pfeifer SP; Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA. |
|---|---|
| Jazyk: | angličtina |
| Zdroj: | Virus evolution [Virus Evol] 2023 Dec 20; Vol. 10 (1), pp. vead083. Date of Electronic Publication: 2023 Dec 20 (Print Publication: 2024). |
| DOI: | 10.1093/ve/vead083 |
| Abstrakt: | The rapid emergence and spread of antimicrobial resistance across the globe have prompted the usage of bacteriophages (i.e. viruses that infect bacteria) in a variety of applications ranging from agriculture to biotechnology and medicine. In order to effectively guide the application of bacteriophages in these multifaceted areas, information about their host ranges-that is the bacterial strains or species that a bacteriophage can successfully infect and kill-is essential. Utilizing sixteen broad-spectrum (polyvalent) bacteriophages with experimentally validated host ranges, we here benchmark the performance of eleven recently developed computational host range prediction tools that provide a promising and highly scalable supplement to traditional, but laborious, experimental procedures. We show that machine- and deep-learning approaches offer the highest levels of accuracy and precision-however, their predominant predictions at the species- or genus-level render them ill-suited for applications outside of an ecosystems metagenomics framework. In contrast, only moderate sensitivity (<80 per cent) could be reached at the strain-level, albeit at low levels of precision (<40 per cent). Taken together, these limitations demonstrate that there remains room for improvement in the active scientific field of in silico host prediction to combat the challenge of guiding experimental designs to identify the most promising bacteriophage candidates for any given application. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.) |
| Databáze: | MEDLINE |
| Externí odkaz: |
|